The drug discovery industry is under increasing pressure to rapidly prioritize compound candidates based on their efficacy and specificity. Although traditional chip based gene expression microarrays can provide significant insights, sample format and throughput considerations preclude more widespread use. Microtiter plate based microarray (MPMA) systems can be directly integrated into the existing drug discovery process and would address the need for high sample throughput multiplexed gene expression assays. Apath LLC, an antiviral drug discovery company, and ProteoPlex, a microtiter plate based microarray company propose a collaboration to develop a multiplexed gene expression assay suitable for drug discovery applications such as toxicant identification. ProteoPlex has developed systems for spotting up to 144 oligonucleotide probes per microtiter well and Apath has well characterized viral replicon systems and cytotoxicity data that facilitate assay validation. We initially plan to optimize assay sensitivity and reproducibility through use of purified in vitro transcripts and modification of the probe deposition, hybridization, and cDNA target labeling conditions. We will next demonstrate that the MPMA can faithfully reproduce dose response effects by focusing on the well characterized interferon mediated inhibition of viral replicon RNAs. Finally, we will demonstrate the utility of the MPMA in identification of active and toxic compounds by performing blinded screens on panels of well-characterized compounds and comparing the results to those obtained in standard cytotoxicity assays. [unreadable] [unreadable]